Deflecting the parasitic paradigm: new insights into mutualistic transposons in plant genomes Inherited transposable elements (TEs) embedded in genomes have an incomparable potential for large-effect mutagenesis. Notwithstanding that transposable elements can be destructive when mobile, it is undeniable that some beneficial effects arise as well. From a population-level perspective, de novo genetic variation arising from TE transposition endows species with increased potential to colonize and thrive in extremely diverse environments. With an emphasis on plant genomes, this review provides an overview of recent insights into functional transpositions and the mechanisms behind them. We will discuss the underappreciated application prospects of mobile elements as prominent endogenous mutagens through recent evidence of transposition-induced phenotypic variation. These novel findings suggest a shift away from the view of TEs as solely parasitic entities and advocate for a more mutualistic role.

Deflecting the parasitic paradigm: new insights into mutualistic transposons in plant genomes #plantscience

Salt stress alters plant development, including the floral transition, but regulation of timing of flowering by salt is poorly understood at the molecular level. To identify genetic loci regulating the floral transition under high soil salinity, we performed a genome-wide association study (GWAS) in Arabidopsis thaliana and identified natural variation at the UGT74E1-UGT74E2-BT3 (UUB) locus that correlates with bolting time specifically in response to salt stress. Genetic analysis revealed BT3 as a novel repressor of the floral transition in control conditions. Similarly, the putative IBA glycosylases UGT74E1 & UGT74E2 delay the floral transition in control conditions. Furthermore, we identified that IBA homeostasis regulators TOB1 and ECH2/IBR10 play a key role in the floral transition, and that ECH2/IBR10 are required for the early flowering phenotype of the ugt74e1/ugt74e2 double mutant, indicating that UGT74E1 & UGT74E2 delay flowering by altering IBA homeostasis. A pangenome analysis of the UUB locus revealed variation in the occurrence of the DNA transposon SAUERKRAUT (SKRT). CRISPR-mediated SKRT deletion in Col-0 affected gene expression both within and outside the UUB locus and caused a salt-dependent delayed floral transition. The delayed bolting phenotype of the skrt-2 mutant also depends on ECH2/IBR10 function, indicating that SKRT accelerates the floral transition by altering IBA homeostasis. Finally, targeted demethylation of SKRT resulted in delayed floral transition under salt stress. Taken together, our data show a role for SKRT and its DNA methylation levels in the salt-dependent bolting time response in Arabidopsis, revealing a novel molecular mechanism to control flowering in adverse conditions.

New bioRxiv preprint!🌱 We found the SAUERKRAUT transposon to regulate the floral transition in a salt-dependent manner!🧂
A step toward salt-tolerant crops in a changing climate!🌞🥬
🔗 doi.org/10.64898/202...
#PlantScience #SaltStress #ClimateChange @pph-wur.bsky.social @christatesterink.bsky.social

I'm a data scientist @ourworldindata.org and I need help from a botanist or someone local to Kyoto, Japan! 🌸

We present one of the world’s longest climate records: 1,200 years of peak cherry blossom dates in Kyoto.

The researcher who maintained it, Prof. Yasuyuki Aono, sadly passed away last year.

Can CRISPR edits enable precise tuning of plant gene expression? We think: yes.

In our newest manuscript, we measured the effects of >30,000 CRISPR-like promoter mutations in sorghum protoplasts.

Unstructured transcription factor interactions enable emergent specificity How intrinsically disordered regions (IDRs) influence chromatin binding and nuclear organization of transcription factors (TFs) remains unclear. We employed proximity-assisted photoactivation (PAPA), ...

Unstructured transcription factor interactions enable emergent specificity www.science.org/doi/10.1126/... - such an interesting paper!

Evolution of a distinct chromatin regulatory landscape in brown algae - Nature Ecology & Evolution Chromatin plays a central role in gene regulation, but chromatin systems are only known for a few model species. This study analyses chromatin regulatory landscapes in brown algal lineages to elucidat...

Chromatin plays a central role in gene regulation, but chromatin systems are only known for a few model species. This study analyses chromatin regulatory landscapes in brown algal lineages to elucidate their structural organization and evolution 🧪 www.nature.com/articles/s41...

Nature’s toxic cocktails Phytochemical mixtures of related molecules with slightly different structures enhance Milkweeds' defense mechanisms against herbivores.

Nature’s toxic cocktails

Transposable elements hitchhike on Starships across fungal genomes - Nature Communications Large mobile genetic elements known as Starships act as vehicles for transferring transposable elements (TEs) between fungi. Here, Griem-Krey et al. show that these ‘hitchhiking’ TEs can drive rapid e...

Now out!
We show that TEs can be horizontally transferred between fungal species via Starships. Once transferred, these TEs can become active, changing the genome organization and affecting the lifestyle of the recipient fungus.
www.nature.com/articles/s41...
@oggenfussursula.bsky.social #TEsky

What have we learned over the past 30 years since the discovery of the first TIR-containing plant immune receptor? Cloning of the necrotic-type response gene (N gene) from Nicotiana glutinosa in the 1990s identified the first Toll/interleukin-1 receptor (TIR)-domain-containing nucleotide-binding domain and leucine-rich repeat (NLR) immune receptor, marking a significant milestone in understanding innate immunity across plants, animals, and, more recently, prokaryotes. N confers resistance to tobacco mosaic virus by detecting the viral p50 helicase domain of the replicase through an N receptor-interacting protein, thereby triggering a hypersensitive response that prevents viral spread. Over the past 30 years, research on N has established it as a key model for studying NLR receptor function, revealing conserved mechanisms in plant–pathogen interactions. Here, we review the complex regulation of NLR-mediated immunity and propose a molecular network that governs immune responses, with implications for engineering disease resistance in crops.

What have we learned over the past 30 years since the discovery of the first TIR-containing plant immune receptor? #plantscience

Plant cell surface receptors Plant cell surface receptors have evolved to perceive peptides, proteins, glycans, lipids, and small molecules through diverse ectodomains, integrating these inputs into distinct physiological output....

Cell-surface receptors play key roles across many biological processes.
In plants, these receptor families have undergone remarkable expansion. Here, we systematically review these receptors in
@theplantjournal.bsky.social

Happy to see this out!
onlinelibrary.wiley.com/doi/10.1111/...

New method paper from Alberto Caregnato and former PhD student @hohmannulrich.bsky.social. A tailored crystallisation screen for plant receptor kinase ectodomains, with examples from our lab and from @cellsensing.bsky.social. Check it out: www.biorxiv.org/content/10.6...

Over 250 million protein sequences are known, but fewer than 0.1% have confirmed functions. Today, @genophoria.bsky.social, @bowang87.bsky.social & team introduce BioReason-Pro, a multimodal reasoning model that predicts protein function and explains its reasoning like an expert would.

Breakthrough study in plant immunity reveals previously unsuspected… The wheat WAI3 receptor forms a novel defence-activating resistosome made of eight molecules, as revealed by an international collaboration led by The Sainsbury Laboratory

Exciting news!

New findings from TSL and international collaborators reveal that the wheat receptor WAI3 forms an octameric resistosome, offering fresh insights into plant immune system structures and functions 🌱

@jonathandgjones.bsky.social @kamounlab.bsky.social

www.tsl.ac.uk/news/breakth...

Frontiers | Alternative splicing: an underexplored layer in immune receptor regulation, systemic resistance and priming Plant immunity relies on precise regulation of pattern-recognition receptors (PRRs) and nucleotide-binding leucine-rich repeat receptors (NLRs). Beyond trigg...

Cool new perspective paper:

Alternative splicing: an underexplored layer in immune receptor regulation, systemic resistance and priming

www.frontiersin.org/journals/pla...

Computational design of conformation-biasing mutations to alter protein functions Conformational biasing (CB) is a rapid and streamlined computational method that uses contrastive scoring by inverse folding models to predict protein variants biased toward desired conformational sta...

Can we design mutations that bias proteins towards desired conformational states?

Today in @science.org, we introduce Conformational Biasing (CB), a simple and scalable computational method that uses contrastive scoring by inverse folding models to identify conformation-biasing mutations.

CAR1 NLR is preferentially expressed in guard cells and mediates stomatal immunity against AvrE1 during invasion (to some P. syringae isolates). www.biorxiv.org/content/10.6...

Very interesting read. I highly recommend it! -> Releasing agriculture from the food security mandate

Impacts of climate extremes on plant pathogens, microbiomes and plant health - Nature Reviews Microbiology In this Review, Singh and colleagues discuss the impacts of key climate extremes on soil-borne pathogens, plant microbiomes and host physiology that ultimately determine disease outcomes, as well as t...

🧪

Molecular gatekeepers: eukaryotic translation factors decoding plant–virus dynamics for resistance engineering - Stress Biology Plant viruses are among the most significant biotic stressors, posing a severe threat to crop productivity and global food security. Their success largely depends on the exploitation of host eukaryoti...

Molecular gatekeepers: eukaryotic translation factors decoding plant–virus dynamics for resistance engineering

Pankhuri Singhal, Shubham Saini ... Jitender Singh, Kalenahalli Yogendra

link.springer.com/article/10.1...

#PlantVirology #Pathogen #Translational #SusceptibilityFactors

Important work in plant genomics by my good friend Idan Efroni in collab with the Zach Lippman

Silence is not golden when it comes to science and AI The scope of scientific inquiry is contracting as research focuses on data-rich problems

An emerging pattern: AI use improves immediate outcomes, a lot, but limits big picture thinking as there is no data for that; this in @financialtimes.com www.ft.com/content/0c63...

Assembly of helper NLR resistosome clusters upon activation of a coiled-coil NLR Nature - SUMM2, a coiled-coil NLR, promotes the assembly of higher-order resistosome clusters to initiate cell death in plants.

Great to see this really cool story published in Nature! rdcu.be/e7UoR
Parker & Wang’s commentary, “A fellowship of the rings in plant defence”, provides further insights into the elaborate structures of NLRs formed during plant immunity. rdcu.be/e7UnA @nature.com @mpipz.bsky.social

Great to see this recommendation. I would love to see something similar in the sciences: AI co-scientists have great potential for knowledge management and to accelerate research, but funding for discovery science and fair compensation is needed for value generation and for equitable access.

AI can write genomes — how long until it creates synthetic life? The Evo2 genomic language model can generate short genome sequences, but scientists say further advances are needed to write genomes that will work inside living cells.

AI can write genomes — how long until it creates synthetic life? www.nature.com/articles/d41...

Building Evo 2: A Frontier DNA Language Model YouTube video by Arc Institute

Evo 2, the largest fully open biological AI model to date, is now published in @nature.com

youtu.be/o_w-E--u7GQ

The rise and fall of peer review Why the greatest scientific experiment in history failed, and why that's a great thing

This is a really thoughtful and interesting article on our current #PeerReview system in #AcademicPublishing by Adam Mastroianni.

Absolutely worth the read. And you can then spend even more time reading the really interesting follow-up articles.

#Science #SciencePublishing #ResearchPublishing

Pathogen-induced red pigmentation uncovers a conserved floral defense in Asteraceae www.biorxiv.org/content/10.64898/2026.02...

Have you ever wondered 🤔... Does phenotypic variance respond to environmental perturbation? Does it have a genetic basis? Are mean and variance regulating loci exposed to different selection pressures? These and more questions are explored in our new preprint 🔥

www.biorxiv.org/content/10.6...

Finding one mutation that improves a protein is hard. Finding five that work together is exponentially harder.

Today in @science.org, Hsu and Konermann labs present MULTI-evolve, a lab-in-the-loop framework that does it in just one machine learning-guided round.

Global status of genome editing versus transgenesis legislation in plants and the current EU situation - npj Science of Plants npj Science of Plants - Global status of genome editing versus transgenesis legislation in plants and the current EU situation

🌍 A new study maps how the 196 UN member states regulate #NGTs.
It outlines 8 differing regulatory approaches and finds that countries allowing transgenic plants are about 23% more likely to approve #GenomeEditing #CRISPR
www.nature.com/articles/s44...